Center for Data-Driven Discovery in Biomedicine

The Center for Data-Driven Discovery in Biomedicine (D³b) is a translational biomedical research Center at Children’s Hospital of Philadelphia, which brings together expertise across disciplines to accelerate bench-to-bedside research on behalf of children. The D³b Center is founded on convergence research principles that define its partnership with other leading researchers, clinicians, and patient advocates, spanning across areas of expertise, across institutions, and across the globe — to collaboratively generate the quantity and quality of information and increased understanding needed to accelerate discoveries and improve treatments for pediatric diseases.  

D³b's open-science model allows the Center to securely generate and integrate large volumes of complex genomic, clinical, and patient data, supported by open-access, D³b-developed platforms that empower collaborative discovery. In addition to its clinical and scientific collaborations, D³b is a champion of the patient community, working alongside more than 50 nonprofit foundations and patient advocates.

The Center is organized into seven main units:

• The Clinical Research Unit (CRU) supports observational and interventional trials including the management of subject enrollment and consent, regulatory, clinical data, and biospecimens. The CRU supports research across the rare disease space, with a specific focus in pediatric brain tumors, epilepsy, and fetal birth defects such as craniofacial abnormalities.
• The Biospecimen Research Unit (BRU), in collaboration with the CHOP Biorepository Core, is responsible for the standardized collection, management and distribution of samples for research and discovery.
• The Data Analytics Management & Engineer Unit (DAMEU) empowers data throughout the entire scientific and translational research process. The unit is structured into two main components, the Bioinformatics Team and the Data Engineering Team. The bioinformatics team members focuses on bioinformatics pipeline engineering, genomics data processing, downstream analysis and interpretation. The data engineering team members are responsible for designing, building and operating software platforms and infrastructure for management, distribution, and scalable analysis of data.
• The Pre-Clinical Laboratory Research Unit (PCLRU) supports the D³b center’s basic and translational research efforts. The PCLRU researches pediatric central nervous system and solid tumors. The primary goal of the unit is to harness patient-centered approaches using translational methodology, including projects focused on basic cell biology explorations, the creation of tumor-derived cell lines, animal models, drug development, and testing.
• The Molecular Diagnostic Research Unit (MDRU) focuses on the research and development of innovative clinical platforms and tests. This unit concentrates its efforts on clinical molecular data generation and analysis of brain tumor biomarkers for direct clinical application. The MDRU works to develop new methods and workflows to improve and optimize clinical diagnostic effectiveness.
• The Strategic Coordination Unit (SCU) provides key expertise in communications, business, financial and grant management, program and project management, strategic planning, operational infrastructure development, human resources and team development and coordination of the execution of over 80 MTA, DUA, contracts and agreements.
• The Translational Imaging Research Unit (TIRU) hosts and manages large-scale, multi-site repositories of biomedical imaging data for researchers at CHOP and around the world as a core center for the Children’s Brain Tumor Network. The goal of this work is to provide researchers access to rich, complex datasets to ultimately accelerate discoveries in pediatric brain cancer and translate results back to patient care in the clinic. TIRU leverages state-of-the-art techniques in artificial intelligence and machine learning to extract complex imaging features and diagnostic biomarkers to perform predictive analytics of clinical measures.

D³b brings together these leading clinical care professionals, data scientists, bioinformaticians, other researchers, and the patient community to discover cures and better therapeutics for children diagnosed with cancer and other diseases.

Research Project Highlights

• Gabriella Miller Kids First Data Resource Center (Kids First DRC): The Gabriella Miller Kids First Data Resource Center is a new, collaborative, pediatric research effort with the goal of understanding the genetic causes of and links between childhood cancer and structural birth defects. Investigators at CHOP, in partnership with the Ontario Institute for Cancer Research, the University of Chicago, Children’s National Health System, the Oregon Health and Science University, and SevenBridges, created a centralized, cloud-based database and discovery portal of well-curated clinical and genetic sequence data from dozens of childhood cancer and structural birth defect cohorts. Data from approximately 8,000 DNA and RNA samples are ready for analysis, and that number is expected to grow to more than 30,000 over the next few years. Find out more about Kids First.

Children's Brain Tumor Network: The Children's Brain Tumor Network CBTN) is a collaborative, multi-institutional research program dedicated to finding new prognostic biomarkers and therapies for the effective treatment of children with brain tumors. CBTN has developed a network of informatics and data applications that allow researchers from across the world to work together to discover cures. CBTN consists of numerous national and international member institutions, with the CBTN operations center located at D3b. and integrates genomic and molecular research, biorepository management, and support for the informatics platforms to provide free and open access to brain tumor data to researchers. Additionally, CBTN has a key collaboration with the Pediatric Neuro-Oncology Consortium, which focuses on conducting clinical trials using a precision medicine approach to accelerate research discovery to help children diagnosed with brain tumors. In September of 2018, CBTN launched the Pediatric Brain Tumor Atlas (PBTA), the world's most comprehensive collection of childhood brain tumor data.

• Cavatica: A scalable, cloud-based platform that allows researchers anywhere in the world to communicate and share data in real time, Cavatica provides comprehensive, integrated access to more than five petabytes of genomic data across adult and pediatric cancers. It integrates functionality across numerous biomedical and informatics applications such as PedCBioPortal, Harvest, and SevenBridges. Cavatica is the primary data analysis and sharing platform for the Gabriella Miller Kids First Data Resource Center. Find out more about how Cavatica supports data analysis and empowers collaboration for discovery in clinical trials and pre-clinical research.